SMTL ID : 8p5u.1

Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum with Coenzyme A bound to the E2o domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.17 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.647, N.680, I.682 Ligands: TPP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.647, A:I.682 MG.5: 4 residues within 4Å: Chain B: D.647, N.680, I.682 Ligands: TPP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.647, B:I.682 MG.9: 4 residues within 4Å: Chain C: D.647, N.680, I.682 Ligands: TPP.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.647, C:I.682 MG.13: 4 residues within 4Å: Chain D: D.647, N.680, I.682 Ligands: TPP.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.647, D:I.682 MG.17: 4 residues within 4Å: Chain E: D.647, N.680, I.682 Ligands: TPP.20 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.647, E:I.682 MG.21: 4 residues within 4Å: Chain F: D.647, N.680, I.682 Ligands: TPP.24 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.647, F:I.682

6 x COA: COENZYME A(Non-covalent)

COA.2: 15 residues within 4Å: Chain A: R.144, K.158, S.160, F.161, T.162, H.163, A.203, Y.235, E.236, R.243, N.261, G.263, G.264, G.285, M.287 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.144, A:R.144, A:E.236, A:R.243, A:N.261, A:G.285, A:M.287 Salt bridges: A:R.144, A:K.158 COA.6: 15 residues within 4Å: Chain B: R.144, K.158, S.160, F.161, T.162, H.163, A.203, Y.235, E.236, R.243, N.261, G.263, G.264, G.285, M.287 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.144, B:R.144, B:Y.235, B:E.236, B:R.243, B:N.261, B:G.285, B:M.287 Salt bridges: B:R.144, B:K.158 COA.10: 14 residues within 4Å: Chain C: R.144, K.158, S.160, F.161, T.162, H.163, A.203, Y.235, E.236, R.243, N.261, G.263, G.285, M.287 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.144, C:E.236, C:R.243, C:N.261, C:G.285, C:M.287 Salt bridges: C:R.144, C:K.158 COA.14: 15 residues within 4Å: Chain D: R.144, K.158, S.160, F.161, T.162, H.163, A.203, Y.235, E.236, R.243, N.261, G.263, G.264, G.285, M.287 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.144, D:R.144, D:Y.235, D:E.236, D:R.243, D:N.261, D:G.285, D:M.287 Salt bridges: D:R.144, D:K.158 COA.18: 15 residues within 4Å: Chain E: R.144, K.158, S.160, F.161, T.162, H.163, A.203, Y.235, E.236, R.243, L.259, N.261, G.263, G.285, M.287 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:R.144, E:R.144, E:E.236, E:R.243, E:N.261, E:G.285, E:M.287 Salt bridges: E:R.144, E:K.158 COA.22: 15 residues within 4Å: Chain F: R.144, K.158, S.160, F.161, T.162, H.163, A.203, Y.235, E.236, R.243, N.261, G.263, G.264, G.285, M.287 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:R.144, F:Y.235, F:E.236, F:R.243, F:N.261, F:G.285, F:M.287 Salt bridges: F:R.144, F:K.158

6 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 19 residues within 4Å: Chain A: T.824, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.1141 Hydrogen bonds: A:T.824, A:G.832, A:T.1037, A:T.1037, A:R.1053, A:S.1092, A:I.1142, A:N.1145, A:N.1145, A:R.1146 Salt bridges: A:H.831, A:K.1089, A:R.1146, A:R.1146 pi-Cation interactions: A:R.1053 ACO.7: 19 residues within 4Å: Chain B: T.824, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.1141 Hydrogen bonds: B:T.824, B:G.832, B:T.1037, B:T.1037, B:R.1053, B:S.1092, B:I.1142, B:N.1145, B:N.1145, B:R.1146 Salt bridges: B:H.831, B:K.1089, B:R.1146, B:R.1146 pi-Cation interactions: B:R.1053 ACO.11: 19 residues within 4Å: Chain C: T.824, L.829, P.830, H.831, G.832, G.1034, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:P.1141 Hydrogen bonds: C:T.824, C:G.832, C:T.1037, C:R.1053, C:S.1092, C:I.1142, C:N.1145, C:N.1145, C:R.1146 Salt bridges: C:H.831, C:K.1089, C:R.1146, C:R.1146 pi-Cation interactions: C:R.1053 ACO.15: 19 residues within 4Å: Chain D: T.824, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.1141, D:P.1141 Hydrogen bonds: D:T.824, D:G.832, D:T.1037, D:T.1037, D:R.1053, D:S.1092, D:I.1142, D:N.1145, D:N.1145, D:R.1146 Salt bridges: D:H.831, D:K.1089, D:R.1146, D:R.1146 pi-Cation interactions: D:R.1053 ACO.19: 18 residues within 4Å: Chain E: T.824, P.830, H.831, G.832, G.1034, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:P.1141 Hydrogen bonds: E:T.824, E:G.832, E:T.1037, E:R.1053, E:S.1092, E:N.1145, E:N.1145, E:R.1146 Salt bridges: E:H.831, E:K.1089, E:R.1146, E:R.1146 pi-Cation interactions: E:R.1053 ACO.23: 18 residues within 4Å: Chain F: T.824, P.830, H.831, G.832, G.1034, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:P.1141 Hydrogen bonds: F:T.824, F:G.832, F:T.1037, F:T.1037, F:R.1053, F:S.1092, F:I.1142, F:N.1145, F:N.1145, F:R.1146 Salt bridges: F:H.831, F:K.1089, F:R.1146, F:R.1146 pi-Cation interactions: F:R.1053

6 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 19 residues within 4Å: Chain A: H.545, R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Chain B: E.903, L.949, E.951, Q.975, F.979 Ligands: MG.1 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.949 pi-Stacking: B:F.979 Hydrogen bonds: A:S.610, A:L.612, A:D.647, A:A.648, A:A.649 Salt bridges: A:H.545, A:R.546 TPP.8: 19 residues within 4Å: Chain A: E.903, L.949, E.951, Q.975, F.979 Chain B: H.545, R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Ligands: MG.5 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.610, B:L.612, B:D.647, B:D.647, B:A.648, B:A.649, B:N.680, B:H.749 Salt bridges: B:H.545, B:R.546 Hydrophobic interactions: A:L.949 pi-Stacking: A:F.979 TPP.12: 19 residues within 4Å: Chain C: H.545, R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Chain D: E.903, L.949, E.951, Q.975, F.979 Ligands: MG.9 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.610, C:L.612, C:D.647, C:A.648, C:A.649 Salt bridges: C:H.545, C:R.546 Hydrophobic interactions: D:L.949 pi-Stacking: D:F.979 TPP.16: 19 residues within 4Å: Chain C: E.903, L.949, E.951, Q.975, F.979 Chain D: H.545, R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Ligands: MG.13 11 PLIP interactions: 2 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:L.949 pi-Stacking: C:F.979 Hydrogen bonds: D:S.610, D:L.612, D:D.647, D:A.648, D:A.649, D:N.680, D:H.749 Salt bridges: D:H.545, D:R.546 TPP.20: 19 residues within 4Å: Chain E: H.545, R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Chain F: E.903, L.949, E.951, Q.975, F.979 Ligands: MG.17 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:S.610, E:L.612, E:D.647, E:A.648, E:A.649 Salt bridges: E:H.545, E:R.546 Hydrophobic interactions: F:L.949 pi-Stacking: F:F.979 TPP.24: 19 residues within 4Å: Chain E: E.903, L.949, E.951, Q.975, F.979 Chain F: H.545, R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Ligands: MG.21 12 PLIP interactions: 2 interactions with chain E, 10 interactions with chain F Hydrophobic interactions: E:L.949 pi-Stacking: E:F.979 Hydrogen bonds: F:S.610, F:L.612, F:D.647, F:D.647, F:A.648, F:A.649, F:N.680, F:H.749 Salt bridges: F:H.545, F:R.546

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L. et al., High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun (2023)

Release Date

2023-08-16

Peptides

2-oxoglutarate dehydrogenase E1/E2 component: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

2-oxoglutarate dehydrogenase E1/E2 component

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